A Proficient Enzyme

Radzicka, Anna; Wolfenden, Richard

doi:10.1126/science.7809611

Cited by 865 publications

(927 citation statements)

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“…As an example, the rate for the uncatalyzed hydrolysis of dimethyl phosphate at 25 xC (Radzicka & Wolfenden, 1995) has an estimated rate constant of approximately 2r10 x13 s x1 . Further complicating studies of phosphate hydrolysis is the fact that the reaction can not only proceed via P-O cleavage but also via C-O cleavage, which, in this case has been shown to be responsible for up to 99% of the reactivity (and is not the site of cleavage by the relevant enzymes).…”

Section: The Mechanism(s) Of Phosphate Diester Hydrolysismentioning

confidence: 99%

Why nature really chose phosphate

Kamerlin

Sharma

Prasad

et al. 2013

Quart. Rev. Biophys.

334

448

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Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, ‘Why Nature Chose Phosphate’ (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that naturereallychose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.

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Section: The Mechanism(s) Of Phosphate Diester Hydrolysismentioning

confidence: 99%

Why nature really chose phosphate

Kamerlin

Sharma

Prasad

et al. 2013

Quart. Rev. Biophys.

334

448

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“…Although there are now many examples which demonstrate how selective encapsulation in a host cavity can enhance the reactivity of a bound guest, all have failed to reach the degree of increased reactivity typical of enzymes. 4 We now report the catalysis of the Nazarov cyclization by a self-assembled coordination cage, a carbon-carbon bond-forming reaction which proceeds under mild, aqueous conditions. The acceleration in this system is over a million-fold, and represents the first example of supramolecular catalysis that achieves the level of rate enhancement comparable to that observed in several enzymes.…”

mentioning

confidence: 99%

“…Competitive binding experiments between Cp*H and the Diels-Alder adduct (4) showed that 4 is a weaker-binding guest, explaining why it does not noticeably retard the reaction rate.…”

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confidence: 99%

Enzymelike Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation

et al. 2010

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A primary goal in the design and synthesis of molecular hosts has been the selective recognition and binding of a variety of guests using non-covalent interactions. 1 Supramolecular catalysis, which is the application of such hosts towards catalysis, 2 has much in common with many enzymatic reactions, 3 chiefly the use of both spatially appropriate binding pockets and precisely oriented functional groups to recognize and activate specific substrate molecules. Although there are now many examples which demonstrate how selective encapsulation in a host cavity can enhance the reactivity of a bound guest, all have failed to reach the degree of increased reactivity typical of enzymes. 4 We now report the catalysis of the Nazarov cyclization by a self-assembled coordination cage, a carbon-carbon bond-forming reaction which proceeds under mild, aqueous conditions. The acceleration in this system is over a million-fold, and represents the first example of supramolecular catalysis that achieves the level of rate enhancement comparable to that observed in several enzymes. We explain the unprecedented degree of rate increase as due to the combination of (a) preorganization of the encapsulated substrate molecule, (b) stabilization of the transition state of the cyclization by constrictive binding, and (c) increase in the basicity of the complexed alcohol functionality.Raymond and coworkers have designed a supramolecular host (1) with Ga 4 L 6 stoichiometry (L = N,N ′ -bis(2,3-dihydroxybenzoyl)-1,5-diaminonaphthalene, Figure 1) that exploits reversible metal-ligand interactions to spontaneously self-assemble. 5 In these assemblies the biscatecholate ligands span the edges of a tetrahedron in which the vertices are occupied by metal ions. Polyanion 1 is soluble in water and other polar solvents, while the host interior is panelled by the naphthalene rings of the ligand, creating a hydrophobic inner environment.A wide variety of cationic guests are encapsulated in 1, from quaternary ammonium and phosphonium cations to organometallic complexes. In aqueous solution, neutral molecules, such as hydrocarbons, are bound by 1 due to the hydrophobic effect. 6 Our approach towards supramolecular catalysis using 1 exploits the polyanionic host's preference for encapsulating monocationic guests. Encapsulation in 1 can perturb acid-base equilibria to favor the protonation of a wide range of amines and phosphines, even at strongly basic pH. 7 These investigations led to the development of proton-catalyzed hydrolysis reactions inside of 1, in which a protonated transition-state is stabilized in the host interior. 8 The stabilization of even transient protonated species produces a several thousandfold rate acceleration of orthoformate and acetal hydrolysis under basic conditions. However, even this substantial acceleration does not reach that typically seen in enzyme-catalyzed reactions.

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“…Hydrogen bonding modulates recognition of DNA and RNA bases, and the interaction energy between two bonded complementary nucleobases is dependent on the intrinsic basicity of the acceptor atoms as well as on the acidity of donor NH groups [1,2]. In addition, understanding the intrinsic reactivity of nucleic bases can shed light on key biosynthetic mechanisms in which nucleobases are substrates [3][4][5][6][7][8].…”

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confidence: 99%

The acidity of uracil and uracil analogs in the gas phase: Four surprisingly acidic sites and biological implications

Kurinovich

Lee

2002

J. Am. Soc. Mass Spectrom.

160

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The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have ⌬H acid values of 331-333 kcal mol Ϫ1 ; the acidity of the N3 sites fall between 347-352 kcal mol Ϫ1 . The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol Ϫ1 , and 369 kcal mol Ϫ1 in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol Ϫ1 . Calculations conducted at B3LYP/6-31ϩG* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed. (J Am Soc Mass Spectrom 2002, 13, 985-995)

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A Proficient Enzyme

Cited by 865 publications

References 31 publications

Why nature really chose phosphate

Why nature really chose phosphate

Enzymelike Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation

The acidity of uracil and uracil analogs in the gas phase: Four surprisingly acidic sites and biological implications

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